Dear Geoff Perhaps you could try jligand available from: http://www.ysbl.york.ac.uk/mxstat/JLigand/index.html
There are few tutorials how to deal with ligands and links. I hope it helps Cheers Garib On 20 May 2011, at 21:59, Geoffrey Feld wrote: > Greetings fellow Crystallographers, > > I'm working on a structure at 1.8-A resolution that contains an acetone > crosslink between 2 cysteines (crosslink was incorporated by adding > 1,3-dichloroacetone). I figured that the easiest way to model this is to > mutate one of the cysteines to S-acetonylcysteine (CSA in the PDB) and then > link it to the other cys. I've seen how to do this in COOT using the > mutate-by-overlap function; however, CSA is of course not in the CCP4 library > that is installed on our system. I've built restraints for CSA using > phenix.elbow and tried importing the residue into COOT that way, still to no > avail. So I figured the way to go now is to import the cif file directly into > the LIBCHECK library in our system and then I should (in theory) be able to > use mutate-by-overlap to place the residue. However, this is where I'm stuck. > I can't seem to figure out the notation for importing the cif file into > LIBCHECK. I tried using FILE_CIF CSA.cif and I get an error "reading title of > input file." What am I doing wrong? Is there another approach I should > consider? Any help or advice would be greatly appreciated. > > > Cheers, > > Geoff > > > > -- > Geoffrey K. Feld > > Department of Chemistry > 492 Stanley Hall > University of California, Berkeley > > "Vigilia pretium libertatis"
